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Oxime side-chain cross-links in the GCN4-p1 dimeric coiled coil: Cyclic product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZTA PDB 2ZTA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.1 M sodium acetate pH 4.6, 1.6 M sodium chloride, 5% w/v PEG 1500; crystal was treated with 1 equiv. sodium periodate relative to protein and allowed to incubate for 2 days prior to harvesting, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.945 α = 93.91 b = 33.102 β = 111.95 c = 41.075 γ = 98.74
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944 Rigaku VariMax Optics 2012-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 28.52 95.2 0.05 9.2 1.9 6255
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB 2ZTA 2.3 28.52 2 6225 319 94.75 0.2603 0.2586 0.2443 0.292 0.2876 RANDOM; THIN RESOLUTION SHELLS
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -7.4926 -1.2921 0.0257 0.1576 5.1161 7.335
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.984 f_angle_d 1.479 f_chiral_restr 0.094 f_bond_d 0.009 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1073 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 26
Software Software Software Name Purpose CrystalClear data collection PHASER phasing PHENIX refinement CrystalClear data reduction CrystalClear data scaling